26 November 2020

This blogpost has been created as part of a lab workshop on using git version control and has been a great excuse to share and discuss interesting papers that have influenced our work!

High Throughput Genetics and Cell Biology

Marah Jnied:

“A Network of Cytosolic Factors Targets SRP-Independent Proteins to the Endoplasmic Reticulum” is a paper that highlights the importance and complexity of SRP-independent translocation. In this paper, Ast, Schuldiner, et al., employ a combination of hydropathy-based analysis and microscopy to identify a determinant for Endoplasmic Reticulum targeting, and to reveal a network of cytosolic proteins that facilitate SRP-independent targeting and translocation. This paper inspired an exciting set of experiments for my PhD project concerning the RNA binding protein Ssd1.

Bioinformatics Papers

Flic Anderson:

“Best Practices for Scientific Computing” pulls together ideas for how to produce readable, shareable code that will deliver reliable results worth publishing. It’s informed by the authors’ involvement in the Carpentries Organisation and it’s inspired me to train as a Carpentries Instructor to help teach data and software workshops as well as using the skills day to day in my developer work on riboviz.

Functional Genomics Papers

Edward Wallace:

“Defining the essential function of yeast Hsf1 reveals a compact transcriptional program for maintaining eukaryotic proteostasis” is a neat paper that takes a hard problem and makes it seem easy. Since the 1980s, it was known that Heat shock factor 1 is an essential gene required for transcription of heat shock protein genes. But it wasn’t known why it was essential - which regulatory targets of Hsf1 are actually relied on by the cell? My then-officemate Eric Solís started working on this, and I had little idea what he was so excited about at the start. His work grew into this elegant story that uses genetics, ChIP-seq, RNA-seq, etc, to dissect Hsf1’s function away from everything else going on. This paper is a great model of how to take a “pleiotropic” regulatory factor and find out its specific regulatory functions.

Some of my lovely Chicago colleagues wrote a perspective on this work - “Heat Shock Factor 1: From Fire Chief to Crowd-Control Specialist”.

Eszter Denes:

“Candida glabrata Drug:H+ Antiporter CgQdr2 Confers Imidazole Drug Resistance, Being Activated by Transcription Factor CgPdr1” describes many experiments that can be conducted in order to show that a particular gene causes antifungal resistance in fungi. What is more, the authors also tested which transcription factor controls this gene’s expression levels. As my PhD project is about antifungal adaptation, I find this paper very informative and inspiring.

Translational Control Papers

Rosey Bayne:

“Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth” is a paper from Mark Ashe’s Lab which shows that, in contrast to P-bodies and stress granules, a subset of RNP granules harbour translated mRNAs under active growth conditions and that these granules are inherited by developing daughter cells, where protein synthesis is most heavily required. I work on Ssd1, an RNA binding protein which translationally represses the cell wall-associated mRNAs it binds, until it is phosphorylated by Cbk1 kinase at or near the bud neck where it is under tight cell-cycle control. This paper suggests that once the Ssd1-associated mRNAs are released from repression they should have access to such translation factories and allow expansion of the bud.